Evolutionary Patterns of Non-Coding RNA in Cardiovascular Biology

Cardiovascular diseases (CVDs) affect the heart and the vascular system with a high prevalence and place a huge burden on society as well as the healthcare system. These complex diseases are often the result of multiple genetic and environmental risk factors and pose a great challenge to understanding their etiology and consequences. With the advent of next generation sequencing, many non-coding RNA transcripts, especially long non-coding RNAs (lncRNAs), have been linked to the pathogenesis of CVD. Despite increasing evidence, the proper functional characterization of most of these molecules is still lacking. The exploration of conservation of sequences across related species has been used to functionally annotate protein coding genes. In contrast, the rapid evolutionary turnover and weak sequence conservation of lncRNAs make it difficult to characterize functional homologs for these sequences. Recent studies have tried to explore other dimensions of interspecies conservation to elucidate the functional role of these novel transcripts. In this review, we summarize various methodologies adopted to explore the evolutionary conservation of cardiovascular non-coding RNAs at sequence, secondary structure, syntenic, and expression level.

Long Non-coding RNAs: At the Heart of Cardiac Dysfunction?

During the past decade numerous studies highlighted the importance of long non-coding RNAs (lncRNAs) in orchestrating cardiovascular cell signaling. Classified only by a transcript size of more than 200 nucleotides and their inability to code for proteins, lncRNAs constitute a heterogeneous group of RNA molecules with versatile functions and interaction partners, thus interfering with numerous endogenous signaling pathways. Intrinsic transcriptional regulation of lncRNAs is not only specific for different cell types or developmental stages, but may also change in response to stress factors or under pathological conditions. Regarding the heart, an increasing number of studies described the critical regulation of lncRNAs in multiple cardiac disorders, underlining their key role in the development and progression of cardiac diseases. In this review article, we will summarize functional cardiac lncRNAs with a detailed view on their molecular mode of action in pathological cardiac remodeling and myocardial infarction. In addition, we will discuss the use of circulating lncRNAs as biomarkers for prognostic and diagnostic purposes and highlight the potential of lncRNAs as a novel class of therapeutic targets for therapeutic purpose in heart diseases.

Expression Profile of Long Noncoding RNAs, lnc-Cox2, and HOTAIR in Rheumatoid Arthritis Patients

Despite the increased proof that long noncoding RNAs (lncRNAs) can control gene expression and broadly affect the normal physiological and disease conditions, the part of lncRNAs in rheumatoid arthritis (RA) is not well known. This study aimed to assess the serum expression levels of lnc-Cox2 and HOTAIR in RA and to investigate their role as novel noninvasive biomarkers in diagnosis of RA. Also, their relations with the levels of interleukin (IL)-6 and matrix metalloproteinase (MMP)-9 and with other clinicolaboratory data in RA patients were analyzed. LncRNAs-Cox2 and HOTAIR expression levels were detected in serum by real-time quantitative polymerase chain reaction. Both IL-6 and MMP-9 levels in serum were measured by enzyme-linked immunosorbent assay. The mRNA expression of lncRNA-Cox2 and HOTAIR was significantly upregulated in RA patients compared with healthy controls. Serum levels of both IL-6 and MMP-9 were significantly higher in RA patients than in healthy subjects (P < 0.001 each). Receiver operating characteristic (ROC) curve demonstrated that lncRNA-Cox2 and HOTAIR could discriminate RA patients from healthy controls. HOTAIR (not lnc-Cox2) was observed to be an independent predictor for RA using multiple logistic regression analysis. We concluded that lnc-Cox2 and HOTAIR serum expression levels can be used as novel noninvasive biomarkers for the diagnosis of RA.

Mitoquinone ameliorates pressure overload-induced cardiac fibrosis and left ventricular dysfunction in mice

Increasing evidence indicates that mitochondrial-associated redox signaling contributes to the pathophysiology of heart failure (HF). The mitochondrial-targeted antioxidant, mitoquinone (MitoQ), is capable of modifying mitochondrial signaling and has shown beneficial effects on HF-dependent mitochondrial dysfunction. However, the potential therapeutic impact of MitoQ-based mitochondrial therapies for HF in response to pressure overload is reliant upon demonstration of improved cardiac contractile function and suppression of deleterious cardiac remodeling. Using a new (patho)physiologically relevant model of pressure overload-induced HF we tested the hypothesis that MitoQ is capable of ameliorating cardiac contractile dysfunction and suppressing fibrosis. To test this C57BL/6J mice were subjected to left ventricular (LV) pressure overload by ascending aortic constriction (AAC) followed by MitoQ treatment (2 µmol) for 7 consecutive days. Doppler echocardiography showed that AAC caused severe LV dysfunction and hypertrophic remodeling. MitoQ attenuated pressure overload-induced apoptosis, hypertrophic remodeling, fibrosis and LV dysfunction. Profibrogenic transforming growth factor-β1 (TGF-β1) and NADPH oxidase 4 (NOX4, a major modulator of fibrosis related redox signaling) expression increased markedly after AAC. MitoQ blunted TGF-β1 and NOX4 upregulation and the downstream ACC-dependent fibrotic gene expressions. In addition, MitoQ prevented Nrf2 downregulation and activation of TGF-β1-mediated profibrogenic signaling in cardiac fibroblasts (CF). Finally, MitoQ ameliorated the dysregulation of cardiac remodeling-associated long noncoding RNAs (lncRNAs) in AAC myocardium, phenylephrine-treated cardiomyocytes, and TGF-β1-treated CF. The present study demonstrates for the first time that MitoQ improves cardiac hypertrophic remodeling, fibrosis, LV dysfunction and dysregulation of lncRNAs in pressure overload hearts, by inhibiting the interplay between TGF-β1 and mitochondrial associated redox signaling.

Noncoding RNAs regulating cardiac muscle mass

Noncoding RNAs, including microRNAs (miRNAs), long noncoding RNAs (lncRNAs), and circular RNAs (circRNAs) play roles in the development and homeostasis of nearly every tissue of the body, including the regulation of processes underlying heart growth. Cardiac hypertrophy can be classified as either physiological (beneficial heart growth) or pathological (detrimental heart growth), the latter of which results in impaired cardiac function and heart failure and is predictive of a higher incidence of death due to cardiovascular disease. Several miRNAs have a functional role in exercise-induced cardiac hypertrophy, while both miRNAs and lncRNAs are heavily involved in pathological heart growth and heart failure. The latter have the potential to act as an endogenous sponge RNA and interact with specific miRNAs to control cardiac hypertrophy, adding another level of complexity to our understanding of the regulation of cardiac muscle mass. In addition to tissue-specific effects, ncRNA-mediated tissue cross talk occurs via exosomes. In particular, miRNAs can be internalized in exosomes and secreted from various cardiac and vascular cell types to promote angiogenesis, as well as protection and repair of ischemic tissues. ncRNAs hold promising therapeutic potential to protect the heart against ischemic injury and aid in regeneration. Numerous preclinical studies have demonstrated the therapeutic potential of ncRNAs, specifically miRNAs, for the treatment of cardiovascular disease. Most of these studies employ antisense oligonucleotides to inhibit miRNAs of interest; however, off-target effects often limit their potential to be translated to the clinic. In this context, approaches using viral and nonviral delivery tools are promising means to provide targeted delivery in vivo.

Targeting Non-coding RNA in Vascular Biology and Disease

Only recently have we begun to appreciate the importance and complexity of the non-coding genome, owing in some part to truly significant advances in genomic technology such as RNA sequencing and genome-wide profiling studies. Previously thought to be non-functional transcriptional “noise,” non-coding RNAs (ncRNAs) are now known to play important roles in many diverse biological pathways, not least in vascular disease. While microRNAs (miRNA) are known to regulate protein-coding gene expression principally through mRNA degradation, long non-coding RNAs (lncRNAs) can activate and repress genes by a variety of mechanisms at both transcriptional and translational levels. These versatile molecules, with complex secondary structures, may interact with chromatin, proteins, and other RNA to form complexes with an array of functional consequences. A body of emerging evidence indicates that both classes of ncRNAs regulate multiple physiological and pathological processes in vascular physiology and disease. While dozens of miRNAs are now implicated and described in relative mechanistic depth, relatively fewer lncRNAs are well described. However, notable examples include ANRIL, SMILR, and SENCR in vascular smooth muscle cells; MALAT1 and GATA-6S in endothelial cells; and mitochondrial lncRNA LIPCAR as a powerful biomarker. Due to such ubiquitous involvement in pathology and well-known biogenesis and functional genetics, novel miRNA-based therapies and delivery methods are now in development, including some early stage clinical trials. Although lncRNAs may hold similar potential, much more needs to be understood about their relatively complex molecular behaviours before realistic translation into novel therapies. Here, we review the current understanding of the mechanism and function of ncRNA, focusing on miRNAs and lncRNAs in vascular disease and atherosclerosis. We discuss existing therapies and current delivery methods, emphasising the importance of miRNAs and lncRNAs as effectors and biomarkers in vascular pathology.

miR-212/132 Cluster Modulation Prevents Doxorubicin-Mediated Atrophy and Cardiotoxicity

Improved therapy of cancer has significantly increased the lifespan of patients. However, cancer survivors face an increased risk of cardiovascular complications due to adverse effects of cancer therapies. The chemotherapy drug doxorubicin is well known to induce myofibril damage and cardiac atrophy. Our aim was to test potential counteracting effects of the pro-hypertrophic miR-212/132 family in doxorubicin-induced cardiotoxicity. In vitro, overexpression of the pro-hypertrophic miR-212/132 cluster in primary rodent and human iPSC-derived cardiomyocytes inhibited doxorubicin-induced toxicity. Next, a disease model of doxorubicin-induced cardiotoxicity was established in male C57BL/6N mice. Mice were administered either adeno-associated virus (AAV)9-control or AAV9-miR-212/132 to achieve myocardial overexpression of the miR-212/132 cluster. AAV9-mediated overexpression limited cardiac atrophy by increasing left ventricular mass and wall thickness, decreased doxorubicin-mediated apoptosis, and prevented myofibril damage. Based on a transcriptomic profiling we identified fat storage-inducing transmembrane protein 2 (Fitm2) as a novel target and downstream effector molecule responsible, at least in part, for the observed miR-212/132 anti-cardiotoxic effects. Overexpression of Fitm2 partially reversed the effects of miR-212/132. Overexpression of the miR-212/132 family reduces development of doxorubicin-induced cardiotoxicity and thus could be a therapeutic entry point to limit doxorubicin-mediated adverse cardiac effects.

Long noncoding RNAs: A new player in the prevention and treatment of diabetic cardiomyopathy?

Diabetic cardiomyopathy (DCM) can cause extensive necrosis of the heart muscle by metabolic disorders and microangiopathy, with subclinical cardiac dysfunction, and eventually progress to heart failure, arrhythmia, and cardiogenic shock; severe patients may even die suddenly. Long noncoding RNAs (lncRNAs) are a class of nonprotein-coding RNAs longer than 200 nucleotides. They have critical roles in various biological processes, including gene expression regulation, genomic imprinting, nuclear-cytoplasmic trafficking, RNA splicing, and translational control. Recent studies indicated that lncRNAs extensively participate in the development of diverse cardiac diseases, such as cardiac ischaemia, hypertrophy, and heart failure. Little is known about lncRNA in DCM. In this review, we summarize the current literature on lncRNAs in DCM studies, aiming to provide new methods for DCM's future prevention and treatment strategies.

Long noncoding RNA Meg3 regulates cardiomyocyte apoptosis in myocardial infarction

Myocardial infarction (MI), with a major process of cardiomyocyte death, remains a leading cause of morbidity and mortality worldwide. To date, it has been shown that lncRNAs play important roles in cardiovascular pathology. However, the detailed studies on lncRNAs regulating cardiomyocyte death in myocardial infarction are still limited. In this study, we found a progressively upregulated expression of Meg3 in mouse injured heart after MI. Gain-of-function and loss-of-function approaches further revealed pro-apoptotic functions of Meg3 in rodent cardiomyocytes. Moreover, Meg3 was directly upregulated by p53 in hypoxic condition, and involved in apoptotic regulation via its direct binding with RNA-binding protein FUS (fused in sarcoma). Afterwards, adult MI mice that underwent intramyocardial injection with adeno-associated virus serotype 9 (AAV9) system carrying Meg3 shRNA showed a significant improvement of cardiac function. Moreover, we also found that MEG3 was increased in clinical heart failure samples, and had conservatively pro-apoptotic function in human cardiomyocytes that were differentiated from the human embryonic stem cells. Together, these results indicate that p53-induced Meg3-FUS complex plays an important role in cardiomyocyte apoptosis post-MI, and its specific knockdown in cardiomyocytes with AAV9 system represents a promising method to treat MI for preclinical investigation.

Roles of long noncoding RNAs in aging and aging complications

Aging is a universal and time dependent complex biological process, characterized by a progressive physiological dysfunction and an increased vulnerability to death. Though the physiological process of aging is still not fully understood, several cellular and molecular mechanisms have been identified. Long noncoding RNAs is a class of regulatory ncRNAs with transcript lengths >200 nucleotides. Discovery of this vast pool of regulators in mammalian genome supplies a new dimension to study and explore the aging process. In this review, we discuss the contribution of lncRNAs in aging and aging complications, and raise interest of serving lncRNAs as biomarkers and potential therapeutic targets to prolong health and ameliorate age-associated diseases. We hope understanding the roles of these high specificity and low conservation regulators in generating age-associated phenotypes might benefit human lifespan.

Short and Long Noncoding RNAs Regulate the Epigenetic Status of Cells

SIGNIFICANCE

The concepts of junk DNA and transcriptional noise are long gone as the existence of noncoding RNAs (ncRNAs) has been tested extensively in recent years. Given that the epigenetic status of cells affects many biological processes, how ncRNAs mechanistically contribute to these processes is of great interest. Recent Advances: Recent studies show that various ncRNAs interact with epigenetic and/or transcription factors to modulate the epigenetic status of cells directly and/or indirectly. There exists growing interest in the field of cardiovascular research to understand the roles of ncRNAs. Due to the large number of ncRNAs in the mammalian genome, only a handful of ncRNAs have been functionally elucidated, which makes it difficult to understand how ncRNAs interact with protein-coding genes and their encoded proteins.

CRITICAL ISSUES

Although the canonical function of microRNAs (miRNAs) to inhibit the translation of protein-coding genes is well established, the number of functionally annotated long noncoding RNAs (lncRNAs) is still small, which is especially true in the heart.

FUTURE DIRECTIONS

Future studies must connect the epigenetic controls of various cellular phenomena by incorporating both miRNAs and lncRNAs. Antioxid. Redox Signal. 29, 832-845.

Long Noncoding RNAs and Cardiac Disease

SIGNIFICANCE

To maintain homeostasis, gene expression has to be tightly regulated by complex and multiple mechanisms occurring at the epigenetic, transcriptional, and post-transcriptional levels. One crucial regulatory component is represented by long noncoding RNAs (lncRNAs), nonprotein-coding RNA species implicated in all of these levels. Thus, lncRNAs have been associated with any given process or pathway of interest in a variety of systems, including the heart. Recent Advances: Mounting evidence implicates lncRNAs in cardiovascular diseases (CVD) and progression and their presence in the blood of heart disease patients indicates that they are attractive potential biomarkers.

CRITICAL ISSUES

Our understanding of the regulation and molecular mechanisms of action of most lncRNAs remains rudimentary. A challenge is represented by their often low evolutionary sequence conservation that limits the use of animal models for preclinical studies. Nevertheless, a growing number of lncRNAs with an impact on heart function is rapidly accumulating. In this study, we will discuss (i) lncRNAs that control heart homeostasis and disease; (ii) concepts, approaches, and methodologies necessary to study lncRNAs in the heart; and (iii) challenges posed and opportunities presented by lncRNAs as potential therapeutic targets and biomarkers.

FUTURE DIRECTIONS

A deeper knowledge of the molecular mechanisms underpinning CVDs is necessary to develop more effective treatments. Further studies are needed to clarify the regulation and function of lncRNAs in the heart before they can be considered as therapeutic targets and disease biomarkers. Antioxid. Redox Signal. 29, 880-901.

Long non-coding RNAs in coronary atherosclerosis

Coronary atherosclerosis (CAS), a leading cause of cardiovascular disease, is a major cause of death worldwide. CAS is a chronic disease in the aorta that can be caused by dyslipidemia, abnormal glucose metabolism, endothelial cell dysfunction, vascular smooth muscle cell (VSMC) or fibrous connective tissue hyperplasia, immune inflammatory reactions, and many other factors. The pathogenesis of CAS is not fully understood, as it is a complex lesion complicated by multiple factors. Damage-response theories have put forward endothelial cell (EC) injury as the initiating factor for CAS; the addition of lipid metabolism disorders may enhance monocyte adhesion, increase the proliferation and migration of fibroblasts and VSMCs, and accelerate the development of CAS. Furthermore, inflammatory and immune responses can create a vicious cycle of endothelial injury, which also plays key roles in the formation of CAS. Therefore, in order to elucidate the mechanisms controlling CAS, it is important to study the etiology of vascular cell dysfunction, abnormal energy and metabolism disorders, and immune and inflammatory reactions. Non-coding RNAs play regulatory roles in the pathogenesis of CAS, especially long non-coding RNAs (lncRNAs); lncRNAs have recently become a major focus for cardiovascular disease mechanisms, as they play numerous roles in the progression of CAS. Therefore, in this review, we discuss the role of lncRNAs in the pathogenesis of coronary CAS, and their role in the prevention and treatment of coronary CAS.

Long non-coding RNAs in the failing heart and vasculature

Following completion of the human genome, it became evident that the majority of our DNA is transcribed into non-coding RNAs (ncRNAs) instead of protein-coding messenger RNA. Deciphering the function of these ncRNAs, including both small- and long ncRNAs (lncRNAs), is an emerging field of research. LncRNAs have been associated with many disorders and a number have been identified as key regulators in the development and progression of disease, including cardiovascular disease (CVD). CVD causes millions of deaths worldwide, annually. Risk factors include coronary artery disease, high blood pressure and ageing. In this review, we will focus on the roles of lncRNAs in the cellular and molecular processes that underlie the development of CVD: cardiomyocyte hypertrophy, fibrosis, inflammation, vascular disease and ageing. Finally, we discuss the biomarker and therapeutic potential of lncRNAs.

Noncoding RNAs in Cardiac Hypertrophy

Cardiac hypertrophy is classified as pathological and physiological hypertrophy. Pathological hypertrophy typically precedes the onset of heart failure, one of the largest contributors to disease burden and deaths worldwide. In contrast, physiological hypertrophy is an adaptive response and protects against adverse cardiac remodeling. Noncoding RNAs (ncRNAs) have drawn significant attention over the last couple of decades, and their dysregulation is increasingly being linked to cardiac hypertrophy and cardiovascular diseases. In this review, we will summarize the profiling, function, and molecular mechanism of microRNAs, long noncoding RNAs, and circular RNAs in pathological cardiac hypertrophy. Additionally, we also review microRNAs responsible for physiological hypertrophy. With better understanding of ncRNAs in cardiac hypertrophy, manipulation of the important ncRNAs will offer exciting avenues for the prevention and therapy of heart failure.

Non-coding RNAs in cardiovascular diseases: diagnostic and therapeutic perspectives

Recent research has demonstrated that the non-coding genome plays a key role in genetic programming and gene regulation during development as well as in health and cardiovascular disease. About 99% of the human genome do not encode proteins, but are transcriptionally active representing a broad spectrum of non-coding RNAs (ncRNAs) with important regulatory and structural functions. Non-coding RNAs have been identified as critical novel regulators of cardiovascular risk factors and cell functions and are thus important candidates to improve diagnostics and prognosis assessment. Beyond this, ncRNAs are rapidly emgerging as fundamentally novel therapeutics. On a first level, ncRNAs provide novel therapeutic targets some of which are entering assessment in clinical trials. On a second level, new therapeutic tools were developed from endogenous ncRNAs serving as blueprints. Particularly advanced is the development of RNA interference (RNAi) drugs which use recently discovered pathways of endogenous short interfering RNAs and are becoming versatile tools for efficient silencing of protein expression. Pioneering clinical studies include RNAi drugs targeting liver synthesis of PCSK9 resulting in highly significant lowering of LDL cholesterol or targeting liver transthyretin (TTR) synthesis for treatment of cardiac TTR amyloidosis. Further novel drugs mimicking actions of endogenous ncRNAs may arise from exploitation of molecular interactions not accessible to conventional pharmacology. We provide an update on recent developments and perspectives for diagnostic and therapeutic use of ncRNAs in cardiovascular diseases, including atherosclerosis/coronary disease, post-myocardial infarction remodelling, and heart failure.

Noncoding RNAs in disease

Noncoding RNAs are emerging as potent and multifunctional regulators in all biological processes. In parallel, a rapidly growing number of studies has unravelled associations between aberrant noncoding RNA expression and human diseases. These associations have been extensively reviewed, often with the focus on a particular microRNA (miRNA) (family) or a selected disease/pathology. In this Mini‐Review, we highlight a selection of studies in order to demonstrate the wide‐scale involvement of miRNAs and long noncoding RNAs in the pathophysiology of three types of diseases: cancer, cardiovascular and neurological disorders. This research is opening new avenues to novel therapeutic approaches.

Deciphering Non-coding RNAs in Cardiovascular Health and Disease

After being long considered as “junk” in the human genome, non-coding RNAs (ncRNAs) currently represent one of the newest frontiers in cardiovascular disease (CVD) since they have emerged in recent years as potential therapeutic targets. Different types of ncRNAs exist, including small ncRNAs that have fewer than 200 nucleotides, which are mostly known as microRNAs (miRNAs), and long ncRNAs that have more than 200 nucleotides. Recent discoveries on the role of ncRNAs in epigenetic and transcriptional regulation, atherosclerosis, myocardial ischemia/reperfusion (I/R) injury and infarction (MI), adverse cardiac remodeling and hypertrophy, insulin resistance, and diabetic cardiomyopathy prompted vast interest in exploring candidate ncRNAs for utilization as potential therapeutic targets and/or diagnostic/prognostic biomarkers in CVDs. This review will discuss our current knowledge concerning the roles of different types of ncRNAs in cardiovascular health and disease and provide some insight on the cardioprotective signaling pathways elicited by the non-coding genome. We will highlight important basic and clinical breakthroughs that support employing ncRNAs for treatment or early diagnosis of a variety of CVDs, and also depict the most relevant limitations that challenge this novel therapeutic approach.

The circulating non-coding RNA landscape for biomarker research: lessons and prospects from cardiovascular diseases

Pervasive transcription of the human genome is responsible for the production of a myriad of non-coding RNA molecules (ncRNAs) some of them with regulatory functions. The pivotal role of ncRNAs in cardiovascular biology has been unveiled in the last decade, starting from the characterization of the involvement of micro-RNAs in cardiovascular development and function, and followed by the use of circulating ncRNAs as biomarkers of cardiovascular diseases. The human non-coding secretome is composed by several RNA species that circulate in body fluids and could be used as biomarkers for diagnosis and outcome prediction. In cardiovascular diseases, secreted ncRNAs have been described as biomarkers of several conditions including myocardial infarction, cardiac failure, and atrial fibrillation. Among circulating ncRNAs, micro-RNAs (miRNAs), long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs) have been proposed as biomarkers in different cardiovascular diseases. In comparison with standard biomarkers, the biochemical nature of ncRNAs offers better stability and flexible storage conditions of the samples, and increased sensitivity and specificity. In this review we describe the current trends and future prospects of the use of the ncRNA secretome components as biomarkers of cardiovascular diseases, including the opening questions related with their secretion mechanisms and regulatory actions.

Non-coding RNA-linked epigenetic regulation in cardiac hypertrophy

Cardiac hypertrophy is an adaptive enlargement of myocardium in response to pressure overload caused various pathological insults, which is accompanied by alteration of a complex cascade of signaling pathways. During the hypertrophy process, many changes occur at cellular level including gene reprogramming by turning off chromatin regulators. Studies from the past decade have demonstrated that the abnormal epigenetic modifications, such as DNA methylation, histone modification, and oxidative modification of nucleic acid, could lead to changes in chromosome structure and cardiac dysfunction. Increasing evidence indicates that non-coding RNAs (ncRNAs) have functional significance in modulating the gene expression during those pathological events in the heart. Emerging evidences have highlighted that ncRNAs might serve as a signal for changing the state of chromatin, however, the knowledge about the ncRNA-linked epigenetic regulatory mechanisms in cardiac pathologies is still largely unexplored. In this review, we summarize the current information on association between ncRNAs and epigenetic modifications in cardiac hypertrophy, and we have discussed their crosstalk. In addition, this review provides insights into their therapeutic and diagnostic potential for treating hypertrophic heart disease.

Role of non-coding RNAs in cardiotoxicity of chemotherapy

The long-time paradoxical situation of non-coding RNAs (ncRNAs) has been terminated for they emerge as executive at full spectrum of gene expression and translation. More recently, it has been demonstrated that some ncRNAs apparently are associated with chemotherapy, causing cardiotoxicity, which taint long-term recovery of patients in growing body of evidence. The current review focused on up-to-date knowledge on regulation change and molecular signaling of ncRNAs, at mean time evaluate their potentials as diagnostic biomarkers or therapeutic targets to monitor and protect cardio function.

Molecular Regulatory Pathways Link Sepsis With Metabolic Syndrome: Non-coding RNA Elements Underlying the Sepsis/Metabolic Cross-Talk

Sepsis and metabolic syndrome (MetS) are both inflammation-related entities with high impact for human health and the consequences of concussions. Both represent imbalanced parasympathetic/cholinergic response to insulting triggers and variably uncontrolled inflammation that indicates shared upstream regulators, including short microRNAs (miRs) and long non-coding RNAs (lncRNAs). These may cross talk across multiple systems, leading to complex molecular and clinical outcomes. Notably, biomedical and RNA-sequencing based analyses both highlight new links between the acquired and inherited pathogenic, cardiac and inflammatory traits of sepsis/MetS. Those include the HOTAIR and MIAT lncRNAs and their targets, such as miR-122, −150, −155, −182, −197, −375, −608 and HLA-DRA. Implicating non-coding RNA regulators in sepsis and MetS may delineate novel high-value biomarkers and targets for intervention.

Non-coding RNAs and exercise: pathophysiological role and clinical application in the cardiovascular system

There is overwhelming evidence that regular exercise training is protective against cardiovascular disease (CVD), the main cause of death worldwide. Despite the benefits of exercise, the intricacies of their underlying molecular mechanisms remain largely unknown. Non-coding RNAs (ncRNAs) have been recognized as a major regulatory network governing gene expression in several physiological processes and appeared as pivotal modulators in a myriad of cardiovascular processes under physiological and pathological conditions. However, little is known about ncRNA expression and role in response to exercise. Revealing the molecular components and mechanisms of the link between exercise and health outcomes will catalyse discoveries of new biomarkers and therapeutic targets. Here we review the current understanding of the ncRNA role in exercise-induced adaptations focused on the cardiovascular system and address their potential role in clinical applications for CVD. Finally, considerations and perspectives for future studies will be proposed.

Long Non-Coding RNAs in Multifactorial Diseases: Another Layer of Complexity

Multifactorial diseases such as cancer, cardiovascular conditions and neurological, immunological and metabolic disorders are a group of diseases caused by the combination of genetic and environmental factors. High-throughput RNA sequencing (RNA-seq) technologies have revealed that less than 2% of the genome corresponds to protein-coding genes, although most of the human genome is transcribed. The other transcripts include a large variety of non-coding RNAs (ncRNAs), and the continuous generation of RNA-seq data shows that ncRNAs are strongly deregulated and may be important players in pathological processes. A specific class of ncRNAs, the long non-coding RNAs (lncRNAs), has been intensively studied in human diseases. For clinical purposes, lncRNAs may have advantages mainly because of their specificity and differential expression patterns, as well as their ideal qualities for diagnosis and therapeutics. Multifactorial diseases are the major cause of death worldwide and many aspects of their development are not fully understood. Recent data about lncRNAs has improved our knowledge and helped risk assessment and prognosis of these pathologies. This review summarizes the involvement of some lncRNAs in the most common multifactorial diseases, with a focus on those with published functional data.

The long noncoding RNA Wisper controls cardiac fibrosis and remodeling

Long noncoding RNAs (lncRNAs) are emerging as powerful regulators of cardiac development and disease. However, our understanding of the importance of these molecules in cardiac fibrosis is limited. Using an integrated genomic screen, we identified Wisper (Wisp2 super-enhancer-associated RNA) as a cardiac fibroblast-enriched lncRNA that regulates cardiac fibrosis after injury. Wisper expression was correlated with cardiac fibrosis both in a murine model of myocardial infarction (MI) and in heart tissue from human patients suffering from aortic stenosis. Loss-of-function approaches in vitro using modified antisense oligonucleotides (ASOs) demonstrated that Wisper is a specific regulator of cardiac fibroblast proliferation, migration, and survival. Accordingly, ASO-mediated silencing of Wisper in vivo attenuated MI-induced fibrosis and cardiac dysfunction. Functionally, Wisper regulates cardiac fibroblast gene expression programs critical for cell identity, extracellular matrix deposition, proliferation, and survival. In addition, its association with TIA1-related protein allows it to control the expression of a profibrotic form of lysyl hydroxylase 2, implicated in collagen cross-linking and stabilization of the matrix. Together, our findings identify Wisper as a cardiac fibroblast-enriched super-enhancer-associated lncRNA that represents an attractive therapeutic target to reduce the pathological development of cardiac fibrosis in response to MI and prevent adverse remodeling in the damaged heart.

The role of long non-coding RNAs in cardiac development and disease

Cells display a set of RNA molecules at one time point, reflecting thus the cellular transcriptional steady state, configuring therefore its transcriptome. It is basically composed of two different classes of RNA molecules; protein-coding RNAs (cRNAs) and protein non-coding RNAs (ncRNAs). Sequencing of the human genome and subsequently the ENCODE project identified that more than 80% of the genome is transcribed in some type of RNA. Importantly, only 3% of these transcripts correspond to protein-coding RNAs, pointing that ncRNAs are as important or even more as cRNAs. ncRNAs have pivotal roles in development, differentiation and disease. Non-coding RNAs can be classified into two distinct classes according to their length; i.e., small (<200 nt) and long (>200 nt) noncoding RNAs. The structure, biogenesis and functional roles of small non-coding RNA have been widely studied, particularly for microRNAs (miRNAs). In contrast to microRNAs, our current understanding of long non-coding RNAs (lncRNAs) is limited. In this manuscript, we provide state-of-the art review of the functional roles of long non-coding RNAs during cardiac development as well as an overview of the emerging role of these ncRNAs in distinct cardiac diseases.

Non-Coding RNA in the Pathogenesis, Progression and Treatment of Hypertension

Hypertension is a complex, multifactorial disease that involves the coexistence of multiple risk factors, environmental factors and physiological systems. The complexities extend to the treatment and management of hypertension, which are still the pursuit of many researchers. In the last two decades, various genes have emerged as possible biomarkers and have become the target for investigations of specialized drug design based on its risk factors and the primary cause. Owing to the growing technology of microarrays and next-generation sequencing, the non-protein-coding RNAs (ncRNAs) have increasingly gained attention, and their status of redundancy has flipped to importance in normal cellular processes, as well as in disease progression. The ncRNA molecules make up a significant portion of the human genome, and their role in diseases continues to be uncovered. Specifically, the cellular role of these ncRNAs has played a part in the pathogenesis of hypertension and its progression to heart failure. This review explores the function of the ncRNAs, their types and biology, the current update of their association with hypertension pathology and the potential new therapeutic regime for hypertension.

Long Non-Coding RNAs in Vascular Inflammation

Less than 2% of the genome encodes for proteins. Accumulating studies have revealed a diverse set of RNAs derived from the non-coding genome. Among them, long non-coding RNAs (lncRNAs) have garnered widespread attention over recent years as emerging regulators of diverse biological processes including in cardiovascular disease (CVD). However, our knowledge of their mechanisms by which they control CVD-related gene expression and cell signaling pathways is still limited. Furthermore, only a handful of lncRNAs has been functionally evaluated in the context of vascular inflammation, an important process that underlies both acute and chronic disease states. Because some lncRNAs may be expressed in cell- and tissue-specific expression patterns, these non-coding RNAs hold great promise as novel biomarkers and as therapeutic targets in health and disease. Herein, we review those lncRNAs implicated in pro- and anti-inflammatory processes of acute and chronic vascular inflammation. An improved understanding of lncRNAs in vascular inflammation may provide new pathophysiological insights in CVD and opportunities for the generation of a new class of RNA-based biomarkers and therapeutic targets.

Chromatin remodelling and epigenetic state regulation by non-coding RNAs in the diseased heart

Epigenetics refers to all the changes in phenotype and gene expression which are not due to alterations in the DNA sequence. These mechanisms have a pivotal role not only in the development but also in the maintenance during adulthood of a physiological phenotype of the heart. Because of the crucial role of epigenetic modifications, their alteration can lead to the arise of pathological conditions. Heart failure affects an estimated 23 million people worldwide and leads to substantial numbers of hospitalizations and health care costs: ischemic heart disease, hypertension, rheumatic fever and other valve diseases, cardiomyopathy, cardiopulmonary disease, congenital heart disease and other factors may all lead to heart failure, either alone or in concert with other risk factors. Epigenetic alterations have recently been included among these risk factors as they can affect gene expression in response to external stimuli. In this review, we provide an overview of all the major classes of chromatin remodellers, providing examples of how their disregulation in the adult heart alters specific gene programs with subsequent development of major cardiomyopathies. Understanding the functional significance of the different epigenetic marks as points of genetic control may be useful for developing promising future therapeutic tools.

Hypoxia-induced long non-coding RNA Malat1 is dispensable for renal ischemia/reperfusion-injury

Renal ischemia-reperfusion (I/R) injury is a major cause of acute kidney injury (AKI). Non-coding RNAs are crucially involved in its pathophysiology. We identified hypoxia-induced long non-coding RNA Malat1 (Metastasis Associated Lung Adenocarcinoma Transcript 1) to be upregulated in renal I/R injury. We here elucidated the functional role of Malat1 in vitro and its potential contribution to kidney injury in vivo. Malat1 was upregulated in kidney biopsies and plasma of patients with AKI, in murine hypoxic kidney tissue as well as in cultured and ex vivo sorted hypoxic endothelial cells and tubular epithelial cells. Malat1 was transcriptionally activated by hypoxia-inducible factor 1-α. In vitro, Malat1 inhibition reduced proliferation and the number of endothelial cells in the S-phase of the cell cycle. In vivo, Malat1 knockout and wildtype mice showed similar degrees of outer medullary tubular epithelial injury, proliferation, capillary rarefaction, inflammation and fibrosis, survival and kidney function. Small-RNA sequencing and whole genome expression analysis revealed only minor changes between ischemic Malat1 knockout and wildtype mice. Contrary to previous studies, which suggested a prominent role of Malat1 in the induction of disease, we did not confirm an in vivo role of Malat1 concerning renal I/R-injury.

LncRNA PFL contributes to cardiac fibrosis by acting as a competing endogenous RNA of let-7d

Rationale: Cardiac fibrosis is associated with various cardiovascular diseases and can eventually lead to heart failure. Dysregulation of long non-coding RNAs (lncRNAs) has recently been recognized as one of the key mechanisms involved in cardiac diseases. However, the potential roles and underlying mechanisms of lncRNAs in cardiac fibrosis have not been explicitly delineated. Methods and Results: Using a combination of in vitro and in vivo studies, we identified a lncRNA NONMMUT022555, which is designated as a pro-fibrotic lncRNA (PFL), and revealed that PFL is up-regulated in the hearts of mice in response to myocardial infarction (MI) as well as in the fibrotic cardiac fibroblasts (CFs). We found that knockdown of PFL by adenoviruses carrying shRNA attenuated cardiac interstitial fibrosis and improved ejection fraction (EF) and fractional shortening (FS) in MI mice. Further study showed that forced expression of PFL promoted proliferation, fibroblast-myofibroblast transition and fibrogenesis in mice CFs by regulating let-7d, whereas silencing PFL mitigated TGF-β1-induced myofibroblast generation and fibrogenesis. More importantly, PFL acted as a competitive endogenous RNA (ceRNA) of let-7d, as forced expression of PFL reduced the expression and activity of let-7d. Moreover, let-7d levels were decreased in the MI mice and in fibrotic CFs. Inhibition of let-7d resulted in fibrogenesis in CFs, whereas forced expression of let-7d abated fibrogenesis through targeting platelet-activating factor receptor (Ptafr). Furthermore, overexpression of let-7d by adenoviruses carrying let-7d precursor impeded cardiac fibrosis and improved cardiac function in MI mice. Conclusion: Taken together, our study elucidated the role and mechanism of PFL in cardiac fibrosis, indicating the potential role of PFL inhibition as a novel therapy for cardiac fibrosis.

Functionally Conserved Noncoding Regulators of Cardiomyocyte Proliferation and Regeneration in Mouse and Human

Background:

The adult mammalian heart has little regenerative capacity after myocardial infarction (MI), whereas neonatal mouse heart regenerates without scarring or dysfunction. However, the underlying pathways are poorly defined. We sought to derive insights into the pathways regulating neonatal development of the mouse heart and cardiac regeneration post-MI.

Methods and Results:

Total RNA-seq of mouse heart through the first 10 days of postnatal life (referred to as P3, P5, P10) revealed a previously unobserved transition in microRNA (miRNA) expression between P3 and P5 associated specifically with altered expression of protein-coding genes on the focal adhesion pathway and cessation of cardiomyocyte cell division. We found profound changes in the coding and noncoding transcriptome after neonatal MI, with evidence of essentially complete healing by P10. Over two-thirds of each of the messenger RNAs, long noncoding RNAs, and miRNAs that were differentially expressed in the post-MI heart were differentially expressed during normal postnatal development, suggesting a common regulatory pathway for normal cardiac development and post-MI cardiac regeneration. We selected exemplars of miRNAs implicated in our data set as regulators of cardiomyocyte proliferation. Several of these showed evidence of a functional influence on mouse cardiomyocyte cell division. In addition, a subset of these miRNAs, miR-144-3p, miR-195a-5p, miR-451a, and miR-6240 showed evidence of functional conservation in human cardiomyocytes.

Conclusions:

The sets of messenger RNAs, miRNAs, and long noncoding RNAs that we report here merit further investigation as gatekeepers of cell division in the postnatal heart and as targets for extension of the period of cardiac regeneration beyond the neonatal period.

Combining cell and gene therapy to advance cardiac regeneration

INTRODUCTION

The characterization of multipotent endogenous cardiac stem cells (eCSCs) and the breakthroughs of somatic cell reprogramming to boost cardiomyocyte replacement have fostered the prospect of achieving functional heart repair/regeneration.

AREAS COVERED

Allogeneic CSC therapy through its paracrine stimulation of the endogenous resident reparative/regenerative process produces functional meaningful myocardial regeneration in pre-clinical porcine myocardial infarction models and is currently tested in the first-in-man human trial. The in vivo test of somatic reprogramming and cardioregenerative non-coding RNAs revived the interest in gene therapy for myocardial regeneration. The latter, together with the advent of genome editing, has prompted most recent efforts to produce genetically-modified allogeneic CSCs that secrete cardioregenerative factors to optimize effective myocardial repair.

EXPERT OPINION

The current war against heart failure epidemics in western countries seeks to find effective treatments to set back the failing hearts prolonging human lifespan. Off-the-shelf allogeneic-genetically-modified CSCs producing regenerative agents are a novel and evolving therapy set to be affordable, safe, effective and available at all times for myocardial regeneration to either prevent or treat heart failure.

Enhancer-associated long non-coding RNA LEENE regulates endothelial nitric oxide synthase and endothelial function

The optimal expression of endothelial nitric oxide synthase (eNOS), the hallmark of endothelial homeostasis, is vital to vascular function. Dynamically regulated by various stimuli, eNOS expression is modulated at transcriptional, post-transcriptional, and post-translational levels. However, epigenetic modulations of eNOS, particularly through long non-coding RNAs (lncRNAs) and chromatin remodeling, remain to be explored. Here we identify an enhancer-associated lncRNA that enhances eNOS expression (LEENE). Combining RNA-sequencing and chromatin conformation capture methods, we demonstrate that LEENE is co-regulated with eNOS and that its enhancer resides in proximity to eNOS promoter in endothelial cells (ECs). Gain- and Loss-of-function of LEENE differentially regulate eNOS expression and EC function. Mechanistically, LEENE facilitates the recruitment of RNA Pol II to the eNOS promoter to enhance eNOS nascent RNA transcription. Our findings unravel a new layer in eNOS regulation and provide novel insights into cardiovascular regulation involving endothelial function.

eNOS expression is dynamically regulated both transcriptionally and post-transcriptionally by various stimuli. Here the authors identify an enhancer-associated lncRNA (LEENE) that is co-regulated with, and enhances eNOS expression.

LncRNA CAIF inhibits autophagy and attenuates myocardial infarction by blocking p53-mediated myocardin transcription

Increasing evidence suggests that long noncoding RNAs (lncRNAs) play crucial roles in various biological processes. However, little is known about the effects of lncRNAs on autophagy. Here we report that a lncRNA, termed cardiac autophagy inhibitory factor (CAIF), suppresses cardiac autophagy and attenuates myocardial infarction by targeting p53-mediated myocardin transcription. Myocardin expression is upregulated upon H₂O₂ and ischemia/reperfusion, and knockdown of myocardin inhibits autophagy and attenuates myocardial infarction. p53 regulates cardiomyocytes autophagy and myocardial ischemia/reperfusion injury by regulating myocardin expression. CAIF directly binds to p53 protein and blocks p53-mediated myocardin transcription, which results in the decrease of myocardin expression. Collectively, our data reveal a novel CAIF-p53-myocardin axis as a critical regulator in cardiomyocyte autophagy, which will be potential therapeutic targets in treatment of defective autophagy-associated cardiovascular diseases.

Cardiovascular Risk Factors and Markers

Cardiovascular risk is assessed for the prediction and appropriate management of patients using collections of identified risk markers obtained from clinical questionnaire information, concentrations of certain blood molecules (e.g., N-terminal proB-type natriuretic peptide fragment and soluble receptors of tumor-necrosis factor-α and interleukin-2), imaging data using various modalities, and electrocardiographic variables, in addition to traditional risk factors.

The lncRNA Plscr4 Controls Cardiac Hypertrophy by Regulating miR-214

Cardiac hypertrophy accompanied by maladaptive cardiac remodeling is the uppermost risk factor for the development of heart failure. Long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) have various biological functions, and their vital role in the regulation of cardiac hypertrophy still needs to be explored. In this study, we demonstrated that lncRNA Plscr4 was upregulated in hypertrophic mice hearts and in angiotensin II (Ang II)–treated cardiomyocytes. Next, we observed that overexpression of Plscr4 attenuated Ang II-induced cardiomyocyte hypertrophy. Conversely, the inhibition of Plscr4 gave rise to cardiomyocyte hypertrophy. Furthermore, overexpression of Plscr4 attenuated TAC (transverse aortic constriction)-induced cardiac hypertrophy. Finally, we demonstrated that Plscr4 acted as an endogenous sponge of miR-214 and forced expression of Plscr4 downregulated miR-214 expression to promote Mfn2 and attenuate hypertrophy. In contrast, knockdown of Plscr4 upregulated miR-214 to induce cardiomyocyte hypertrophy. Additionally, luciferase assay showed that miR-214 was the direct target of Plscr4, and overexpression of miR-214 counteracted the anti-hypertrophy effect of Plscr4. Collectively, these findings identify Plscr4 as a negative regulator of cardiac hypertrophy in vivo and in vitro due to its regulation of the miR-214-Mfn2 axis, suggesting that Plscr4 might act as a therapeutic target for the treatment of cardiac hypertrophy and heart failure.

Identification and analysis of a key long non-coding RNAs (lncRNAs)-associated module reveal functional lncRNAs in cardiac hypertrophy

Cardiac hypertrophy (CH) is a common disease that originates from long-term heart pressure overload and finally leads to heart failure. Recently, long non-coding RNAs (lncRNAs) have attracted attention because they have broad and crucial functions in regulating complex biological processes. Some studies had found that lncRNAs play vital roles in complex cardiovascular diseases. However, the function and mechanism of lncRNAs in CH have not been elucidated. In our study, to investigate the potential roles of lncRNAs in CH, the Cardiac Hypertrophy-associated LncRNAs-Protein coding genes Network (CHLPN) was constructed by integrating gene microarray re-annotation and subpathway enrichment analyses. After performing random walking with restart in CHLPN, we predicted 21 significant risk lncRNAs, of which 7 (Kis2, 1700110K17Rik, Gm17501, E330017L17Rik, C630043F03Rik, Gm9866 and Ube4bos1) formed a close module with their co-expressed protein-coding genes (PCGs). We found that the module might play crucial roles in the development of CH. In particular, 44 PCGs that were co-expressed with six lncRNAs were enriched in CH-related biological processes and pathways. We also found that some lncRNAs participated in the competitive endogenous RNA cross-talk that might be involved in CH. These results indicate that the functional lncRNAs are related to post-transcriptional regulation and could shed light on a new molecular diagnostic target of CH.

Valsartan regulates TGF-β/Smads and TGF-β/p38 pathways through lncRNA CHRF to improve doxorubicin-induced heart failure

This study investigated the interaction among valsartan (VAL), TGF-β pathways, and long non-coding RNA (lncRNA) cardiac hypertrophy-related factor (CHRF) in doxorubicin (DOX)-induced heart failure (HF), and explored their roles in DOX-induced HF progression. HF mice models in vivo were constructed by DOX induction. The expression of CHRF and TGF-β1 in hearts was detected, along with cardiac function, caspase-3 activity, and cell apoptosis. Primary myocardial cells were pretreated with VAL, followed by DOX induction in vitro for functional studies, including the detection of cell apoptosis with terminal deoxynucleotidyl transferase dUTP nick-end labeling and the expression of proteins associated with TGF-β1 pathways. HF models were established in vivo and in vitro. Expression of CHRF and TGF-β1 was up-regulated, and cell apoptosis and caspase-3 activity were increased in the hearts and cells of the HF models. VAL supplementation alleviated the cardiac dysfunction and injury in the HF process. Moreover, overexpressed CHRF up-regulated TGF-β1, promoted myocardial cell apoptosis, and reversed VAL's cardiac protective effect, while interference of CHRF (si-CHRF) did the opposite. Down-regulation of CHRF reversed the increased expression of TGF-β1 and the downstream proteins induced by pcDNA-TGF-β1 in HL-1 cells, while overexpression of CHRF reversed the VAL's cardiac protective effect in vivo. In conclusion, VAL regulates TGF-β pathways through lncRNA CHRF to improve DOX-induced HF.